Browsing by Subject "Biochemistry & Molecular Biology"

Now showing 1 - 9 of 9
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    Challenges encountered during development of Mn porphyrin-based, potent redox-active drug and superoxide dismutase mimic, MnTnBuOE-2-PyP5+, and its alkoxyalkyl analogues
    (JOURNAL OF INORGANIC BIOCHEMISTRY, 2017-04-01) Rajic, Zrinka; Tovmasyan, Artak; de Santana, Otávio L; Peixoto, Isabelle N; Spasojevic, Ivan; do Monte, Silmar A; Ventura, Elizete; Rebouças, Júlio S; Batinic-Haberle, Ines
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    DNA barcoding exposes a case of mistaken identity in the fern horticultural trade.
    (Molecular ecology resources, 2010-11) Pryer, Kathleen M; Schuettpelz, Eric; Huiet, Layne; Grusz, Amanda L; Rothfels, Carl J; Avent, Tony; Schwartz, David; Windham, Michael D
    Using cheilanthoid ferns, we provide an example of how DNA barcoding approaches can be useful to the horticultural community for keeping plants in the trade accurately identified. We use plastid rbcL, atpA, and trnG-R sequence data to demonstrate that a fern marketed as Cheilanthes wrightii (endemic to the southwestern USA and northern Mexico) in the horticultural trade is, in fact, Cheilanthes distans (endemic to Australia and adjacent islands). Public and private (accessible with permission) databases contain a wealth of DNA sequence data that are linked to vouchered plant material. These data have uses beyond those for which they were originally generated, and they provide an important resource for fostering collaborations between the academic and horticultural communities. We strongly advocate the barcoding approach as a valuable new technology available to the horticulture industry to help correct plant identification errors in the international trade.
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    Erratum to "Manganese porphyrin redox state in endothelial cells: Resonance Raman studies and implications for antioxidant protection towards peroxynitrite" [Free Radic. Biol. Med. 126 (2018) 379-392].
    (Free radical biology & medicine, 2018-12) Carballal, Sebastián; Valez, Valeria; Alvarez-Paggi, Damián; Tovmasyan, Artak; Batinic-Haberle, Ines; Ferrer-Sueta, Gerardo; Murgida, Daniel H; Radi, Rafael
    © 2018 Elsevier Inc. The publisher regrets in Fig. 4, the legend does not correspond to that Figure, as it was incorrectly duplicated from the legend of Fig. 2 during the production process. The correct legend of Fig. 4 is as follows. The publisher would like to apologise for any inconvenience caused.
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    High-speed widefield photoacoustic microscopy of small-animal hemodynamics.
    (Biomedical optics express, 2018-10) Lan, Bangxin; Liu, Wei; Wang, Ya-Chao; Shi, Junhui; Li, Yang; Xu, Song; Sheng, Huaxin; Zhou, Qifa; Zou, Jun; Hoffmann, Ulrike; Yang, Wei; Yao, Junjie
    Optical-resolution photoacoustic microscopy (OR-PAM) has become a popular tool in small-animal hemodynamic studies. However, previous OR-PAM techniques variously lacked a high imaging speed and/or a large field of view, impeding the study of highly dynamic physiologic and pathophysiologic processes over a large region of interest. Here we report a high-speed OR-PAM system with an ultra-wide field of view, enabled by an innovative water-immersible hexagon-mirror scanner. By driving the hexagon-mirror scanner with a high-precision DC motor, the new OR-PAM has achieved a cross-sectional frame rate of 900 Hz over a 12-mm scanning range, which is 3900 times faster than our previous motor-scanner-based system and 10 times faster than the MEMS-scanner-based system. Using this hexagon-scanner-based OR-PAM system, we have imaged epinephrine-induced vasoconstriction in the whole mouse ear and vascular reperfusion after ischemic stroke in the mouse cortex in vivo, with a high spatial resolution and high volumetric imaging speed. We expect that the hexagon-scanner-based OR-PAM system will become a powerful tool for small animal imaging where the hemodynamic responses over a large field of view are of interest.
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    Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability
    (MOLECULAR CELL, 2011-08-05) Mukherjee, Neelanjan; Corcoran, David L; Nusbaum, Jeffrey D; Reid, David W; Georgiev, Stoyan; Hafner, Markus; Ascano, Manuel; Tuschl, Thomas; Ohler, Uwe; Keene, Jack D
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    Learned sensing: jointly optimized microscope hardware for accurate image classification.
    (Biomedical optics express, 2019-12) Muthumbi, Alex; Chaware, Amey; Kim, Kanghyun; Zhou, Kevin C; Konda, Pavan Chandra; Chen, Richard; Judkewitz, Benjamin; Erdmann, Andreas; Kappes, Barbara; Horstmeyer, Roarke
    Since its invention, the microscope has been optimized for interpretation by a human observer. With the recent development of deep learning algorithms for automated image analysis, there is now a clear need to re-design the microscope's hardware for specific interpretation tasks. To increase the speed and accuracy of automated image classification, this work presents a method to co-optimize how a sample is illuminated in a microscope, along with a pipeline to automatically classify the resulting image, using a deep neural network. By adding a "physical layer" to a deep classification network, we are able to jointly optimize for specific illumination patterns that highlight the most important sample features for the particular learning task at hand, which may not be obvious under standard illumination. We demonstrate how our learned sensing approach for illumination design can automatically identify malaria-infected cells with up to 5-10% greater accuracy than standard and alternative microscope lighting designs. We show that this joint hardware-software design procedure generalizes to offer accurate diagnoses for two different blood smear types, and experimentally show how our new procedure can translate across different experimental setups while maintaining high accuracy.
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    Oxidative stress promotes SIRT1 recruitment to the GADD34/PP1α complex to activate its deacetylase function.
    (Cell death and differentiation, 2018-02) Lee, Irene Chengjie; Ho, Xue Yan; George, Simi Elizabeth; Goh, Catherine Wenhui; Sundaram, Jeyapriya Rajameenakshi; Pang, Karen Ka Lam; Luo, Weiwei; Yusoff, Permeen; Sze, Newman Siu Kwan; Shenolikar, Shirish
    Phosphorylation of the eukaryotic translation initiation factor, eIF2α, by stress-activated protein kinases and dephosphorylation by the growth arrest and DNA damage-inducible protein (GADD34)-containing phosphatase is a central node in the integrated stress response. Mass spectrometry demonstrated GADD34 acetylation at multiple lysines. Substituting K315 and K322 with alanines or glutamines did not impair GADD34's ability to recruit protein phosphatase 1α (PP1α) or eIF2α, suggesting that GADD34 acetylation did not modulate eIF2α phosphatase activity. Arsenite (Ars)-induced oxidative stress increased cellular GADD34 levels and enhanced Sirtuin 1 (SIRT1) recruitment to assemble a cytoplasmic complex containing GADD34, PP1α, eIF2α and SIRT1. Induction of GADD34 in WT MEFs paralleled the dephosphorylation of eIF2α (phosphoserine-51) and SIRT1 (phosphoserine-47). By comparison, eIF2α and SIRT1 were persistently phosphorylated in Ars-treated GADD34-/- MEFs. Expressing WT GADD34, but not a mutant unable to bind PP1α in GADD34-/- MEFs restored both eIF2α and SIRT1 dephosphorylation. SIRT1 dephosphorylation increased its deacetylase activity, measured in vitro and in cells. Loss of function of GADD34 or SIRT1 enhanced cellular p-eIF2α levels and attenuated cell death following Ars exposure. These results highlighted a novel role for the GADD34/PP1α complex in coordinating the dephosphorylation and reactivation of eIF2α and SIRT1 to determine cell fate following oxidative stress.
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    Pharmacokinetics, Brain Hippocampus and Cortex, and Mitochondrial Accumulation of a New Generation of Lipophilic Redox-Active Therapeutic, Mn(III) Meso Tetrakis(N-n-butoxyethylpyridinium-2-yl)porphyrin, MnTnBuOE-2-PyP5+, in Comparison with its Ethyl and N-hexyl Analogs, MnTE-2-PyP5+ and MnTnHex-2-PyP5+
    (Free Radical Biology and Medicine, 2013-11) Spasojevic, Ivan; Weitner, Tin; Tovmasyan, Artak; Sheng, Huaxin; Miriyala, Sumitra; Leu, David; Rajic, Zrinka; Warner, David S; Clair, Daret St; Huang, Ting-Ting; Batinic-Haberle, Ines
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    Wide-field whole eye OCT system with demonstration of quantitative retinal curvature estimation
    (Biomedical Optics Express, 2019-01-01) McNabb, Ryan P; Polans, James; Keller, Brenton; Jackson-Atogi, Moseph; James, Charlene L; Vann, Robin R; Izatt, Joseph A; Kuo, Anthony N